BN1878 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
WM 9.9908e-05 5.6157e-02
Layer 3 9.5080e-04 2.1494e-03
Layer 4 3.2784e-03 5.4975e-03
Layer 5 4.3721e-03 7.7977e-03
Layer 6 4.9000e-03 1.9813e-02
Layer 2 1.2137e-02 1.9340e-02

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
GNB1 Expression Distribution
Gene Specificity Score (GSS)
GNB1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
GNB1 Layer 4 2.7275 0.5298
TOMM20 Layer 3 2.5664 0.5235
KIF1A Layer 5 2.4395 0.5176
MORF4L1 Layer 4 2.5361 0.5112
RTN3 Layer 5 2.3809 0.5090
GDI1 Layer 3 2.9082 0.5083
PJA2 Layer 3 2.5391 0.5080
ATP6V0C Layer 5 2.3867 0.5069
FAIM2 Layer 4 2.7217 0.5050
PRNP Layer 2 2.1348 0.5041
STMN1 Layer 5 2.1055 0.5024
YWHAZ Layer 4 3.1387 0.4996
WBP2 Layer 5 2.1914 0.4961
CYCS Layer 4 2.2744 0.4948
SOD1 Layer 5 2.2227 0.4944
TSC22D1 Layer 3 2.8906 0.4942
NORAD Layer 3 2.2832 0.4930
SIRPA Layer 3 2.5039 0.4915
SNCA Layer 5 3.0859 0.4912
PGRMC1 Layer 5 2.4941 0.4909
FKBP8 Layer 5 2.3867 0.4872
CLIP3 Layer 2 2.9502 0.4869
ARHGEF7 Layer 5 2.0723 0.4869
ATP1A1 Layer 3 3.0312 0.4854
GNAO1 Layer 5 2.5000 0.4852
SERPINI1 Layer 4 3.1113 0.4835
ARPP19 Layer 2 2.7334 0.4830
ATP6V1E1 Layer 5 2.5391 0.4830
GNB2 Layer 3 2.3926 0.4818
GPI Layer 3 3.1631 0.4817
ATP9A Layer 3 2.5723 0.4807
UQCRH Layer 4 2.7998 0.4807
PFN2 Layer 4 2.8281 0.4805
ARL6IP1 Layer 3 2.7539 0.4800
PKM Layer 5 2.6191 0.4799
PREPL Layer 3 2.9531 0.4780
ARF1 Layer 2 2.6660 0.4776
PPIA Layer 2 2.0449 0.4769
VAMP2 Layer 6 2.3242 0.4766
SEZ6L2 Layer 3 2.5664 0.4766
ITM2C Layer 2 2.3076 0.4763
UBC Layer 4 2.2520 0.4758
BAALC Layer 3 2.2949 0.4748
SORL1 Layer 3 2.7598 0.4745
AK5 Layer 2 2.8965 0.4744
ZFAND5 Layer 5 2.4785 0.4741
MAPK1 Layer 2 2.9609 0.4734
SARAF Layer 5 2.4336 0.4733
DCTN1 Layer 3 2.2490 0.4731
TERF2IP Layer 3 2.2637 0.4730

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1878
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1878_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1878/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1878/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1878/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1878/report/PD/BN1878_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1878/report/PD/BN1878_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 09:21:58
  • Number of Processes: 10
  • Spending Time: 0h 4m